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Introduction:

An Update on the Informatics Supported Annotation and Integration of Datasets for the Gynecologic Disease Program (GDP).

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Introduction:

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  1. An Update on the Informatics Supported Annotation and Integration of Datasets for the Gynecologic Disease Program (GDP) Waqas Amin MD1, Sambit K. Mohanty MD1&7, Anil V. Parwani MD PhD1&3, Sharon B. Winters MS1, Nancy B. Whelan BS1, Althea M. Schneider BS1, John T. Milnes BS1, Charma D. Chaussard BS4, Gail Harger MS2, Katherine Farrow BS2, Debra Bass MS2, Tim D. Fennell MS1, Hai Hu PhD6, Thomas C. Krivak MD4, Rajiv Dhir MD3, Robert P. Edwards MD4, Larry Maxwell MD5 Michael J. Becich MD PhD1&3, 1Department of Biomedical Informatics and 2Department of Epidemiology, University of Pittsburgh, PA. USA. 3Department of Pathology and 4Department of Obstetrics Gynecology, Magee-Women Hospital, University of Pittsburgh Medical Center, PA USA. 5Walter Reed Army Medical Center, Washington, DC. USA. 6Windber Research Institute Windber, PA, USA. 7Winthrop University Hospital, New York, USA

  2. Introduction: • The Gynecologic Disease Program (GDP), a.k.a Gynecologic Cancer Center, is funded by the Department of Defense (DOD). • Primary objective is to develop state-of-the-art capabilities in clinical and basic science research aimed at improving screening, early detection, prevention, and treatment of gynecologic disease. • Collaborators: Walter Reed Army Medical Center, University of Pittsburgh Cancer Institute, Windber Research Institute and Georgetown Medical Center. • At UPitt this program constitutes three cores: • Luminex • Proteomics • Tissue Banking Informatics

  3. Objectives: • To create a well-characterized and standard-based biospecimen repository for Ovarian and Endometrial malignancies. • To facilitate the collection and transfer of well annotated datasets to the central data warehouse (Windber Research Institute). • To create an internal storage system of transferred data using the Clinical Trial Management Application (CTMA).

  4. Common Data Elements • Through the combined efforts of experts from various fields, Common Data Elements (demographic, epidemiologic, clinical, pathologic specimen and block annotation, genotype, follow up and outcome) were developed for gynecological conditions. • Common Data Elements (CDEs) allow consistency and interoperability in biospecimen collection and better understanding of research and experimental data. • Major standards used to build CDEs: • College of American Pathology (CAP) checklists • Elements from coPath-synoptics • North American Association of Cancer Registry (NAACR) core elements

  5. PATHOLOGY DATA (coPATH and Synoptics – CAP Checklist) • GDP # (for patient) • Date of Surgery • Surgical Procedure • Macroscopic Attributes • - Anatomic Location • - Size • Microscopic Attributes • - Histologic Type • - Grade (Silverberg grade • etc.) • - Perifocal reaction • - Nodal status • - Pathologic Stage • OVARIAN TUMORS EXTRAOVARIAN ABDOMINAL TUMORS ENDOMETRIAL TUMORS OTHERS (HYPERPLASIAS)

  6. CANCER REGISTRY DATA ELEMENTS (NAACCR STANDRARD) • GDP # (for patient) • Date of Surgery • Surgical Procedure • Clinical Staging (AJCC Staging) • Therapy related variables • Recurrence / Metastasis attributes • Vital status • Biochemical data - Tumor markers - Hormone receptors • OVARIAN TUMORS EXTRAOVARIAN ABDOMINAL TUMORS ENDOMETRIAL TUMORS OTHERS (HYPERPLASIAS)

  7. Core Data Sources: Pathological Evaluation (coPATH and synoptic) Questionnaire Data Cancer Registry System Clinical Trial Management Application De-identified Data Export Central Data Center (WRI)

  8. Questionnaire Data: • Pre-operative Case/Control Matching • Postoperative Questionnaire • HOPE Ovarian • Endometrial

  9. Pathology Data ( coPATH & Synoptics) • Synoptic worksheet are implemented for use in data acquisition. This provides a structured way of entering the diagnostic / prognostic information for particular pathology specimen and ultimately serves as medium for capturing and storing data for translational research. • The data is stored as discrete data elements which appear as an accession summary within the final pathology report. • The synoptic data is manually or electronically imported into the CTMA for linking pathological details on banked tissues.

  10. UPMC Cancer Registry • The UPMC Registry Information Services (RIS) is designed for the collection, management and analysis of demographic, grading, staging, treatment and progression data on cancer patients • Primary sources for documentation are both the “paper” and “electronic” medical records from which data is abstracted into the Cancer Registry database by Certified Cancer Registrars. • The entire UPMC RIS is built on the North American Association of Central Cancer Registries (NAACCR) data standard architecture.

  11. CANCER REGISTRY DATA ELEMENTS (NAACCR STANDRARD) Treatment • Data imported from Cancer Registry Tool. • Data entry done at source application (IMPAC) by cancer registrars. Follow Up Recurrence

  12. Technology: • Clinical Trial Management Application is a web-based Java application for managing various aspects of clinical trails, research protocols and outcome initiatives. • Provides an integrated set of components for managing administrative and regulatory tracking (e.g., IRB-related issues). • Facilitates study protocol schema, treatment calendar and financial management issues for capturing study specific patient information. • Used for internal storage of data in GDP study.

  13. Result: • At UPMC (Magee Women’s Hospital) total number of consented patients is 109. Endometrial cancer (45), ovarian cancer (13), withdrew from the project (33), benign conditions (12), and the rest are pending for surgical procedures. • Patient privacy protection is of utmost importance and is enforced in accordance with Health Insurance Portability and Accountability Act (HIPAA) and only de-identified is transferred to WRI • Well-structured study protocol is implemented for the acquisition of high quality and well characterized annotated biospecimens and transfer of data to central data warehouse (WRI).

  14. Overall Workflow for GDP

  15. Overall Workflow for GDP Patient consented by Research Nurse Coordinator (RNC) and enrolled in GDP study. RNC assigns a GDP Number to the patient, or case, fills out the Paper-based and Web-based (Clinical Trials Management Application [CTMA]) Pre-operative Case/Control Matching Questionnaire, and collects blood sample.

  16. Overall Workflow for GDP Patient undergoes operation and surgical specimen is accessioned for pathological examination (generating coPATH Data). Biospecimen are stored in Magee women Hospital Tissue bank tissue bank and data is Stored in TBINV BENIGN MALIGNANT Post-operative blood sample collected. CASE COMPLETE FROM GDP STUDY

  17. Workflow for GDP Hope Survey RNC completes Paper-based and Web-based (CTMA) Post-operative questionnaire (HOPE for Ovarian / Endometrial post-operative questionnaire) and collects blood sample. RNC MAKES A COPY OF ENTIRE QUESTIONNAIRE DATA & SENDS THE ORIGINAL AND THE COPY TO THE FOLLOWING: ORIGINAL COPY Data Manager, Department of Epidemiology, University of Pittsburgh Department of Biomedical Informatics (DBMI) and Cancer Registry Team Scansoft Processing

  18. Workflow for GDP Data Transfer Transfer Electronic version of Questionnaire Data (Excel layout) to Windber Research Institute (WRI) and send one copy to DBMI. #1 Scansoft CSV Output Files

  19. Workflow for GDP CTMA Annotation DBMI post-doctoral fellows enter pathology data into CTMA (internal use) which is pulled into Excel layout for WRI. Medical Registry data directly pulled for transfer to WRI (Excel layout). Tissue bank inventory data is pulled out in Excel format and transfer to WRI

  20. Workflow for GDP Excel File Generation Transfer Pathology and Registry Data to WRI #2

  21. Conclusion: • The Gynecologic Disease Program acts as a central repository for clinically annotated gynecological tumor tissues for the research community. • This tissue banking initiative provides an infrastructure of joint multi-institutional bioinformatics network that facilitates the sharing of clinically annotated data and high quality biospecimens to support important research activities. • With information gained from these research activities, we will continue to improve screening, early detection, prevention, and treatment of gynecologic disease.

  22. Collaborators: Walter Reed Army Medical Center University of Pittsburgh Cancer Institute Windber Research Institute Georgetown Medical Center Leadership Dr. Ronald Herberman Dr. Michael Becich Dr. Robert Edwards Dr. Larry Maxwell Dr. Rajiv Dhir Dr. Michael Feldman Dr. Anil Parwani Acknowledgments

  23. THANK YOU

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